2P0R - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF HUMAN CALPAIN 9 IN COMPLEX WITH LEUPEPTIN

Authors :   T. L. Davis, R. Paramanathan, J. R. Walker, C. Butler-Cole, P. J. Finert J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkare Paganon, Structural Genomics Consortium (Sgc)

Date :   01 Mar 07 (Deposition) - 20 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,D,E

Keywords :   Inhibitor Complex; Alpha-Beta Protein; Hydrolase; Calcium-Dependent Enzyme; Structural Genomics; Structural Genomics Consortium; Sgc, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. L. Davis, R. Paramanathan, J. R. Walker, C. Butler-Cole, P. J. Finerty Jr. , J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Structures Of Human Minicalpains Bound To Inhibitors
To Be Published
PubMed: search

Molecule 1 - CALPAIN-9
	Chains	:	A, B
	EC Number	:	3.4.22.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-LIC
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	MINICALPAIN
	Gene	:	CAPN9, NCL4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DIGESTIVE TRACT-SPECIFIC CALPAIN; NCL-4; CG36 PROTEIN

Molecule 2 - LEUPEPTIN
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	AR7	2	Mod. Amino Acid	AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3	CA	5	Ligand/Ion	CALCIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:284 , ASP B:291 , LEU B:312 , ASP B:314 , GLU B:316	BINDING SITE FOR RESIDUE CA B 1001
2	AC2	SOFTWARE	GLU A:284 , ASP A:291 , LEU A:312 , ASP A:314 , GLU A:316 , HOH A:1068	BINDING SITE FOR RESIDUE CA A 1002
3	AC3	SOFTWARE	LEU A:81 , GLY A:83 , ASP A:88 , GLU A:167 , HOH A:1007 , HOH A:1168	BINDING SITE FOR RESIDUE CA A 1003
4	AC4	SOFTWARE	LEU B:81 , GLY B:83 , ASP B:88 , GLU B:167	BINDING SITE FOR RESIDUE CA B 1004
5	AC5	SOFTWARE	ARG A:60	BINDING SITE FOR RESIDUE CA A 1005
6	AC6	SOFTWARE	GLN A:91 , GLY A:95 , CYS A:97 , TRP A:98 , LYS A:188 , GLY A:189 , GLY A:190 , PHE A:233 , GLU A:243 , GLY A:253 , HOH A:1149 , GLN B:62 , ARG B:297	BINDING SITE FOR CHAIN D OF LEUPEPTIN
7	AC7	SOFTWARE	GLU A:59 , GLY B:95 , ASP B:96 , CYS B:97 , TRP B:98 , LYS B:188 , GLY B:189 , GLY B:190 , PHE B:233 , SER B:242 , GLY B:253 , HOH B:1105	BINDING SITE FOR CHAIN E OF LEUPEPTIN

(no "SS Bond" information available for 2P0R)

(no "Cis Peptide Bond" information available for 2P0R)

Asymmetric/Biological Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022188	A	102	V	CAN9_HUMAN	Polymorphism	12562749	A/B	A	102	V
2	UniProt	VAR_022189	S	122	R	CAN9_HUMAN	Polymorphism	28359608	A/B	S	122	R
3	UniProt	VAR_022190	D	164	N	CAN9_HUMAN	Polymorphism	28359632	A/B	D	164	N
4	UniProt	VAR_022191	I	234	T	CAN9_HUMAN	Polymorphism	28359644	A/B	I	234	T
5	UniProt	VAR_022192	A	239	T	CAN9_HUMAN	Polymorphism	28359647	A/B	A	239	T
6	UniProt	VAR_022193	R	277	W	CAN9_HUMAN	Polymorphism	28359655	A/B	R	277	W
7	UniProt	VAR_022194	K	322	Q	CAN9_HUMAN	Polymorphism	1933631	A/B	K	322	Q
8	UniProt	VAR_022195	H	327	Q	CAN9_HUMAN	Polymorphism	28359684	A/B	H	327	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CALPAIN_CAT	PS50203	Cysteine proteinase, calpain-type, catalytic domain profile.	CAN9_HUMAN	42-337	2	A:42-337 B:42-337
2	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CAN9_HUMAN	91-102	2	A:91-102 B:91-102

Asymmetric/Biological Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000271971	1a	ENSE00001070036	chr1:230883130-230883455	326	CAN9_HUMAN	1-71	71	2	A:19-71 B:19-71	53 53
1.2	ENST00000271971	2	ENSE00000921431	chr1:230891083-230891152	70	CAN9_HUMAN	72-95	24	2	A:72-95 B:72-95	24 24
1.3	ENST00000271971	3	ENSE00000961374	chr1:230895258-230895376	119	CAN9_HUMAN	95-134	40	2	A:95-134 B:95-134	40 40
1.4	ENST00000271971	4	ENSE00000961375	chr1:230898399-230898532	134	CAN9_HUMAN	135-179	45	2	A:135-179 B:135-179	45 45
1.5	ENST00000271971	5	ENSE00000961376	chr1:230903287-230903455	169	CAN9_HUMAN	179-235	57	2	A:179-235 B:179-235	57 57
1.6	ENST00000271971	6	ENSE00000961377	chr1:230904926-230905009	84	CAN9_HUMAN	236-263	28	2	A:236-263 B:236-263	28 28
1.7	ENST00000271971	7	ENSE00000961378	chr1:230907760-230907845	86	CAN9_HUMAN	264-292	29	2	A:264-292 B:264-292	29 29
1.8	ENST00000271971	8	ENSE00000961379	chr1:230910300-230910377	78	CAN9_HUMAN	292-318	27	2	A:292-318 B:292-318	27 27
1.9	ENST00000271971	9	ENSE00000961380	chr1:230914719-230914879	161	CAN9_HUMAN	318-372	55	2	A:318-337 B:318-337	20 20
1.10	ENST00000271971	10	ENSE00000961381	chr1:230915925-230916082	158	CAN9_HUMAN	372-424	53	0	-	-
1.11	ENST00000271971	11	ENSE00000961382	chr1:230916246-230916454	209	CAN9_HUMAN	425-494	70	0	-	-
1.12	ENST00000271971	12	ENSE00000961383	chr1:230921727-230921763	37	CAN9_HUMAN	494-506	13	0	-	-
1.13	ENST00000271971	13	ENSE00000961384	chr1:230923268-230923348	81	CAN9_HUMAN	507-533	27	0	-	-
1.14	ENST00000271971	14	ENSE00000961385	chr1:230925878-230925935	58	CAN9_HUMAN	534-553	20	0	-	-
1.15a	ENST00000271971	15a	ENSE00000961386	chr1:230927610-230927674	65	CAN9_HUMAN	553-574	22	0	-	-
1.16	ENST00000271971	16	ENSE00000961387	chr1:230928172-230928240	69	CAN9_HUMAN	575-597	23	0	-	-
1.17	ENST00000271971	17	ENSE00000961388	chr1:230928596-230928674	79	CAN9_HUMAN	598-624	27	0	-	-
1.18	ENST00000271971	18	ENSE00000961389	chr1:230930909-230931025	117	CAN9_HUMAN	624-663	40	0	-	-
1.19	ENST00000271971	19	ENSE00001416134	chr1:230933908-230933966	59	CAN9_HUMAN	663-682	20	0	-	-
1.20b	ENST00000271971	20b	ENSE00001414530	chr1:230937316-230937518	203	CAN9_HUMAN	683-690	8	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:319
 aligned with CAN9_HUMAN | O14815 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:319
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
           CAN9_HUMAN    19 ARITHSSGQSFEQMRQECLQRGTLFEDADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
               SCOP domains d2p0ra_ A: Calpain large subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh..........hhhhhh.........eeehhhhhh..........hhhhh......hhhhhhhhhhhh.hhhhhhhhh............eeeeeeee..eeeeeeee..eee...............hhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhh..eeeee.hhh..hhhhhhhhhhhh..eeeee....hhhhh.............eeeeeeeeeee..eeeeeeeee...............hhhhhhhhhhhhhhh........eeeeehhhhhhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------V-------------------R-----------------------------------------N---------------------------------------------------------------------T----T-------------------------------------W--------------------------------------------Q----Q---------- SAPs(SNPs)
                PROSITE (1) -----------------------CALPAIN_CAT  PDB: A:42-337 UniProt: 42-337                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:19-71 UniProt: 1-71 [INCOMPLETE]   Exon 1.2  PDB: A:72-95  ---------------------------------------Exon 1.4  PDB: A:135-179 UniProt: 135-179    --------------------------------------------------------Exon 1.6  PDB: A:236-263    Exon 1.7  PDB: A:264-292     -------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.3  PDB: A:95-134 UniProt: 95-134 --------------------------------------------Exon 1.5  PDB: A:179-235 UniProt: 179-235                --------------------------------------------------------Exon 1.8  PDB: A:292-318   ------------------- Transcript 1 (2)
                 2p0r A  19 ARITHSSGQSFEQMRQECLQRGTLFEDADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with CAN9_HUMAN | O14815 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:319
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
           CAN9_HUMAN    19 ARITHSSGQSFEQMRQECLQRGTLFEDADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
               SCOP domains d2p0rb_ B: Calpain large subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh..........hhhhhh.........eeehhhhhh..........hhhhh......hhhhhhhhhhhhhhhhhhhhhh............eeeeeeee..eeeeeeee..eeee..ee..........hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhh.eeeeee.hhh..hhhhhhhhhhhh..eeeee......................eeeeeeeeeee..eeeeeeeee...............hhhhh..hhhhhh..........eeeeehhhhhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------V-------------------R-----------------------------------------N---------------------------------------------------------------------T----T-------------------------------------W--------------------------------------------Q----Q---------- SAPs(SNPs)
                PROSITE (1) -----------------------CALPAIN_CAT  PDB: B:42-337 UniProt: 42-337                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: B:19-71 UniProt: 1-71 [INCOMPLETE]   Exon 1.2  PDB: B:72-95  ---------------------------------------Exon 1.4  PDB: B:135-179 UniProt: 135-179    --------------------------------------------------------Exon 1.6  PDB: B:236-263    Exon 1.7  PDB: B:264-292     -------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.3  PDB: B:95-134 UniProt: 95-134 --------------------------------------------Exon 1.5  PDB: B:179-235 UniProt: 179-235                --------------------------------------------------------Exon 1.8  PDB: B:292-318   ------------------- Transcript 1 (2)
                 2p0r B  19 ARITHSSGQSFEQMRQECLQRGTLFEDADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLT 337
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2p0r D 355 xLLx 358
                            |  |
                          355-ACE
                             358-AR7

Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2p0r E 355 xLLx 358
                            |  |
                            |  |
                          355-ACE
                             358-AR7

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Calpain large subunit, catalytic domain (domain II) (19)

Protein domain: Calpain large subunit, catalytic domain (domain II) (19)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2p0ra_	A:
1b	d2p0rb_	B:

(no "CATH Domain" information available for 2P0R)

(no "Pfam Domain" information available for 2P0R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CAN9_HUMAN | O14815)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004198	calcium-dependent cysteine-type endopeptidase activity	Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p0r)

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	2p0r
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	CAN9_HUMAN \| O14815
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	3.4.22.52
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	CAN9_HUMAN \| O14815	:	1ziv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (2, 4)

Exons (9, 18)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (11, 11)

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